MolNFT v1 · #112022 · protein + DNA
Fab structure of antibody S1-15 in complex with ssdna DNA, 5'-P5(DT)P- 3'
4Z8F · S1-15 Fab (IGG2B) heavy chain: “Fab structure of antibody S1-15 in complex with ssdna DNA, 5'-P5(DT)P- 3'”. X-ray diffraction, 1 ligand (THP), 7 pockets (best druggability 0.61). MolNFT v1 #112022 on GenesisL1: 3D structure, binding…
- PDB
- 4Z8F
- Type
- protein + DNA
- Length
- 444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S1-15 Fab (IGG2B) heavy chain; S1-15 Fab (IGG2B kappa) light chain…
- Ligands
- THP
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S1-15 Fab (IGG2B) heavy chain | protein | 226 | 8% helix, 50% strand | — |
| L | S1-15 Fab (IGG2B kappa) light chain | protein | 214 | 7% helix, 50% strand | — |
| E | 5'-D(P*TP*TP*TP*TP*T)-3' | dna | 3 | — | — |
| A | 5'-D(P*TP*TP*TP*TP*T)-3' | dna | 1 | — | — |
Ligands and binding sites
- THP · Thymidine-3',5'-diphosphate · ligand · chains H, L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.61 | 0.74 | 60 | empty |
| 2 | 230 | 0.56 | 0.79 | 34 | empty |
| 3 | 61 | 0.45 | 0.83 | 22 | empty |
| 4 | 86 | 0.34 | 0.74 | 19 | empty |
| 5 | 86 | 0.32 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2010 Ų buried · 21 hydrogen bonds · protein-protein
- H–E · 318 Ų buried · 10 hydrogen bonds · protein-nucleic
- H–A · 77 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4Z8F · Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3' · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4Z8F · PDBe 4Z8F
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